To start with, it isn't the "cliche" that's the problem. It's the "overused low-effort" usage of the cliches that is the problem.
Tropes exist for a reason. A good writer and game programmer will make the tropes interesting and unique and offer their own adherence or subversion to those tropes.
A bad one just makes those tropes really cringe. Or annoying. Or "overused".
I mean, compare something like "Hunger Games" to "Battle Royale" and you can instantly tell who the better author was. Or, compare "Batman" to "Iron Man" and you can see the two different spins on "hero can do whatever they want 'cause they got all the money in the world".
It isn't he cliche that's the problem, its how it's used and executed.
But, if you want a list of things I'm tired of seeing:
1. Unjustified angst. Why does every angsty teen have to be Sousuke from Naruto? Dude is literally a terrible person who should've been killed off as the first villain for having a very poor outlook on life, very bad life goals, and the inability to empathize with anyone. He's a literal psychopath/sociopath and not only did he survive to the end of the series, but he's now been emulated by every other low-effort writer on the planet who wants make an "Edgelord" character or a "dark and brooding guy". Dark and brooding is cool. Batman is cool. Sousuke is a crap character who should be a villain, but was hauled across the finish line by "hero" characters with IQ's that don't even chart double digits.
If you can't make your "Edgelord" compelling to a 35 year old beyond "sex appeal" (I know some people out there that just like the Edge Lords at 35 'cause they're so in love with dating the "bad boy" and ruining their lives... but this shouldn't be a writing goal to appeal to THAT audience... unless you're writing smut), then don't write one.
2. The "dainty pure of heart woman healer". Thanks for acknowlding that this type of person would be absolutely useless in any and every way possible... except they can heal people! Man, if they couldn't heal people, they'd just be worthless and usless to everything!
Is there seriously nobody willing to challenge this trope, or do anything interesting with it? The last time I saw anything "interesting" done with it was FFX where it's revealed that Yuna is only the "dainty and pure of heart woman healer" because she has resigned herself to die in order to save the world, and she wants to be as kind and accomodating to everyone as she can possibly be so that her last moments in the world are filled with joy and smiles. We learn that the Yuna we've been interacting with the entire time is just her "facade". It's the brave face she puts on for "the good of the world", rather than "what she actually wants".
Seriously, why can't we do anything with this trope like that? Or, I dunno... make the Healer a big burly muslce-head who is basically just a "personal trainer" or "gym rat" or something, and he got into living healthy because it's hard to watch people accept his healing, but die early anyway from things like heart attacks or whatever. Give him an existential crisis of "Yes, you can heal people, but those people are going to die in a few years anyway from living unhealthy lifestyles or being in dangerous lines of work". That could be fun and interesting.
Do something with this trope! I'm not looking for waifu! You can write compelling waifu without making them avatars of purity and lightness and also useless!
3. "This is not even my final form!". Look guys... the only reason to really engage in this... is that you want to "surprise" the player. It's so overdone that it's no longer a "surprised". Honestly, I'd be more surprised if a boss went, "This isn't even my final form!" and actually was legitimately permanently defeated without ever adopting another form.
I don't know how you'd innovate this trope off the top of my head, but there's probably a way to do it.
While we're at it, I'm adding "...but can you withstand my ultimate attack?!". Look guys, this is basically the "it's not even my final form!" version of a boss... without actually creating a new form. Why isn't your boss using all their most powerful stuff at the beginning of the fight?
I get that we like going, "well, you have to do escalation in storytelling". Yes and no. They're legit trying to kill you, why aren't they blowing every attack possible at the beginning to defeat you, rather than letting you land dozens of hits on them?
This is probably why I like "overpowered heroes" so much as a trope in anime. If a hero can wipe out the threat in a single wave of his hand... I'm more impressed that he does that, rather than beating around the bush for 900 freakin' episodes. I'm also very impressed when villains do it too. If a villain can casually wipe cities off the map, I'd like them to be doing that without using it as a threat... just... you know... do it 'cause they heard the hero was there.
There ARE actual stakes to be had when villains and heroes "don't hold back".
Imagine the villain is wiping out every single town he hears your heroes have been to. Well, now, you gotta keep a very low profile. Gotta be careful who knows who you are. Gotta be careful nobody talks about you to anyone. The citizenry might also view you as a threat since just showing up in town means they all die. THERE ARE STAKES HERE.
I ain't a fan of "let me take forever to use my best stuff, when I'm already almost dead".
Do you know when "The Ultimate Attack" is interesting? Kung Fu Panda. "That's the Wuxi Finger Hold!" "Oh, you know this hold? (mirroring the words his master told him, with the same smirk)" "You're bluffing, Shifu didn't teach you that!" "You're right. (enemy is visibly relieved, but remains in the hold) I figured it out. (insane levels of panic set in on the enemy) Skidoosh. (attack executes).
That's how you do an "ultimate attack". Or... let's say... the 5 Point Exploding Heart Technique from Kill Bill.
There's a way to do it that is awesome and a way to do it that is lame. Most people opt for "lame".
4. McGuffin Contrivances. I'm just going to use Lord of the Rings. "We need to haul this cursed ring to this very specific volcano in order to destroy it!". Why? Are you SERIOUS that it can't be ANY OTHER volcano? I'd head in a direction AWAY from enemy threats, toward a different volcano that isn't guarded. But, you know, THAT'S ME. Likewise, why couldn't the heat from the Balrog melt the dang thing? What if you grafted other nonsense onto the ring, does its power change or alter? What if you casted it into a block of gold so nobody could wear it? Is there also a reason we can't dump it into the deepest part of the ocean where the pressure alone would crumple it like tissue paper? If it has a protection spell on it, is there a reason we can't dispel magic in a setting that clearly allows people to dispel magic?
I just don't like when the McGuffin is full of contrivances and nonsense. If you have a McGuffin, I'd like it to have very clearly defined rules so that I can't start poking plot holes in everything. If you can't manage that... just don't have a McGuffin.
5. Nobody in the world is doing anything to stop whatever the conflict is... except our intrepid heroes.
I don't know why this annoys me, but it does. I sort of like when other people are attempting to solve the problem as well as me. It breathes life into the world. Makes me feel like the NPC's have their own goals and reasons for existing. Other than, just, you know... information dumps for our band of 6 heroes.
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Anyway, that's my short list.... I've got a bunch more, but most of my annoyances with "tropes" typically just comes down to "people are just really bad writers" and isn't an actual problem with the trope itself.